Problem with --al-con : empty output file

  • Hello,

    I'm totally new with Bowtie.
    I have mate pair reads and I would like to filtered those that have a precise orientation.
    Here is the command line I used :
    bowtie2 PG21 -p 12 -q -1 MP1.fastq -2 MP2.fastq -phred33-quals  -minins 1500 -maxins 2500 -no-mixed -no-dovetail -no-contain -no-overlap -rf  -al-con reads_aligned_Rconcordant.fa

    My problem is everything seems to be ok except that the fasta output file is empty…
    Can you help me ? What did I do wrong ?
    How can I get the reads sequences that aligned the way I want ?

    Thank you in advance for your help.